Chemistry
Pyrimidine
Pyrimidine is a heterocyclic aromatic organic compound composed of a six-membered ring with four carbon atoms and two nitrogen atoms. It is a fundamental component of nucleic acids such as DNA and RNA, where it pairs with purines to form the building blocks of genetic material. Pyrimidine derivatives are also important in pharmaceuticals and agrochemicals.
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eBook - ePubNew Frontiers in Nanochemistry: Concepts, Theories, and Trends
Volume 1: Structural Nanochemistry
- Mihai V. Putz, Mihai V. Putz, Mihai Putz(Authors)
- 2020(Publication Date)
- Apple Academic Press(Publisher)
CHAPTER 41Pyrimidines
NICOLETA A. DUDAŞ and MIHAI V. PUTZ
Laboratory of Computational and Structural Physical Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timişoara, Pestalozzi Str. No. 16, Timişoara 300115, Romania, E-mails: [email protected] , [email protected] , [email protected]41.1 DEFINITION
Pyrimidines (1,3-diazines or m-diazines) are one of three classes of six-membered heterocyclic aromatic compounds containing two nitrogen atoms in their ring, the other two diazines being pyridazines (1,2-diazines) and pyrazines (1,4-diazines). The Pyrimidine ring is the basic structural element of nitrogenous bases of DNA and RNA, is one of the most widespread heterocyclic in various biologically important derivatives, as substituted derivatives and ring-fused compounds.Pyrimidine derivatives are utilized as drugs in the treatment of several types of diseases, agrochemicals, chromophores, complexes, metal sensors, solar cells technology, etc. Pyrimidines can be obtained by the synthetic chemical route, from biosynthesis (metabolism ↔ catabolism) and also in prebiotic condition.Because the Pyrimidine ring contains two nitrogen atoms it has a weakly basic character, Pyrimidine systems are highly electron deficient, and that is why electrophilic aromatic substitution gets more difficult, while nucleophilic aromatic substitution gets easier.41.2 HISTORICAL ORIGIN(S)
The first pyrimidinic compounds that were discovered are alloxan – 1818, guanine – 1844, barbituric acid – 1864, cytosine – 1894, uracil – 1900, and in 1899 was first synthesized unsubstituted Pyrimidine (Figure 41.1 ) (Brown et al., 1994; Harris & Thimann, 1949; Grimaux, 1879; Fischer, 1897; Kossel & Steudel, 1903; Gabriel & Colman, 1899; Baeyer, 1864). The first simple Pyrimidine derivatives that have been extracted from natural sources are vicine and convicine in 1870 from Vicia sativa and Vicia faba L
eBook - PDF- Ivor Smith, J. W. T. Seakins, Ivor Smith, J. W. T. Seakins(Authors)
- 2013(Publication Date)
- Butterworth-Heinemann(Publisher)
CHAPTER 8 PURINES, PyrimidineS & RELATED COMPOUNDS V. 0. Oberholzer T H E purines and Pyrimidines and their derivatives are of great impor-tance in biochemistry because of their role as constituents of coenzymes and of nucleic acids. In the form of the nucleic acids the purine and Pyrimidine nucleotides both play an equal and central role in the expres-sion and transmission of genetic information. The metabolism of purines, which represents the major pathway of nitrogen excretion in uricotelic organisms has been extensively studied for many years, due largely to the fact that the end product, uric acid, occurs in high levels which are diagnostic in all forms of gout. (1) In contrast, the study of the pyrimi-dine pathway has only more recently become important following the discovery of metabolic errors involving Pyrimidine synthesis and altera-tions in their excretion in certain diseases. (2 » 3 > 4) The unit structure of the complex molecules of nucleic acids are the mononucleotides which may be represented as Phosphate group - pentose - purine or Pyrimidine base The pentose part may be either D-ribose or 2-deoxy-D-ribose, normally attached to the base by a N-glycosidic bond, and the resulting polymer complexes are termed ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). The commonly found bases in the nucleic acids are, in RNA, adenine, guanine, uracil and cytosine and in DNA, adenine, guanine, cytosine and thymine, and in addition 5-methyl cytosine is found particularly in plant DNA. (5) In the term nucleotide the nitrogenous base, though usually a hetero-cyclic ring as a purine or a Pyrimidine, may have a more simple struc-ture such as glycinamide or an amino group itself. The phosphate group is attached to the hydroxyl group on the 2', 3' or 5' carbon atom of the sugar.
eBook - ePub- S. P. Bhutani(Author)
- 2019(Publication Date)
- CRC Press(Publisher)
The function and structure of a number of enzymes possessing the Pyrimidine ring have been established. Purines can also be strictly considered as Pyrimidine derivatives. Deoxyribonucleic acid contains adenine and guanine.B. Aromatic Character of Pyrimidine
All the parent diazine ring systems may be regarded as aromatic. This conclusion has been derived from the experimental observations of the C—C and C—N bond lengths which have been found to be intermediate in length between the values expected for the characteristic single and double bond in question.In case of simple Pyrimidine, the dimensions have not be determined yet, although a number of derivatives have been studied in this connection. An example is 4-amino-2,6-dichloroPyrimidine. The bond distances are given in its structure below. Out of the two C—C bond distances (1.40 Å and 1.35 Å) one is very close to the C—C distance of benzene (1.39 Å).The general similarity of the size and shape of the Pyrimidine ring to that of benzene and pyridine is consistent with its highly aromatic chemical characteristics. Thus, Pyrimidine also undergoes the usual electrophilic substitution reactions.The differences between the bond angles and bond distances between the ring systems suggest that there is maximum distortion in the case of Pyrimidine. This is in agreement with the resonance energies calculated by molecular orbital methods. The values are benzene 36 K cal, pyridine = 31 K cal and Pyrimidine = 26 K cal/mole.Pyrimidine is best considered as a resonance hybrid of eight structures, out of which only two are uncharged structures. The p-electron densities at the 2, 4 and 5-positions have been calculated as 0.776, 0.825 and 1.103 respectively.C. Chemical Properties of Pyrimidine
An enormous amount of work has been done on the derivatives of Pyrimidines but the chemical reactions of Pyrimidine itself have been investigated only recently. This is partly because Pyrimidine was not readily available. However, it can now be obtained quite easily.
eBook - PDF- Glenn Dryhurst(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
Pyrimidines I. INTRODUCTION, NOMENCLATURE, AND STRUCTURE Pyrimidines in various guises appear in all living cells and are vitally involved in many biological processes, although like purines (which themselves can be considered as Pyrimidine derivatives) they are rarely found in the free state. Rather, they are found as constituents of much larger molecules. Pyrimidines have a six-membered unsaturated ring containing two hetero-cyclic nitrogen atoms separated by a single carbon atom. For this reason Pyrimidines are occasionally known as m-diazines. Structure I illustrates the Pyrimidine ring structure and the numbering system that will be employed here. Several numbering systems have been used, but for the sake of clarity the structure and numbering system shown here will be employed throughout this and other relevant chapters. Many Pyrimidines, especially those of biological interest, are known by trivial names. A number of these compounds, along with their structures and chemical and trivial names, are shown in Table 4-1. It can be seen from these data that in general the oxygen-containing Pyrimidines exist 4 (I) 186 4 Introduction, Nomenclature, and Structure 187 TABLE 4-1 Nomenclature and Structure of Some Common Pyrimidines Trivial name Structure Typical chemical name 0 Pyrimidine N ^ M Pyrimidine; L JJ 1,3-diazine H Ο Uracil H — N |1 2,4-DioxyPyrimidine; 1 ^ JJ 2,4-Pyrimidinediol; 0 Ν 2,4(1tt,3A7)-Pyrimidine-H dione Cytosine | I H 2 2-Oxy-4-aminoPyrimidine; N < ^ 4-amino-2-pyrimidinol; J (I 4-amino-2(1 Ay)-pyrimidinone I Η Ο C H 3 Thymine H N |T 2,4-Dioxy-5-methyl-y Pyrimidine; 0 1 5-methyluracil H Ο Alloxan Η _ Ν ^ ^ · ° 2,4,5,6-TetraoxyPyrimidine; (mesoxalylurea) L 2,4,5,6(1 H.3H)-O Ν 0 Pyrimidinetetrone I Η Ο Barbituric acid H -N ^ ^ I ^ H Ma I ο ny I urea; Ϊ L 6-hydroxyuracil; 0 ^ N ^ 0 2,4,6-Pyrimidinetriol; I 2,4,6(1 A/,3tf,5/V)-H Pyrimidinetrione a As found, for example, in Chemical Abstracts.
eBook - PDF- Desmond J. Brown(Author)
- 2009(Publication Date)
- Wiley-Interscience(Publisher)
(1962, 1970, 1985),6163 and Walker (1989).6164 Reviews of some specific aspects of Pyrimidine chemistry are noted in appropri- ate sections of this book. 1.2. NOMENCLATURE The vagaries of organic chemical nomenclature, especially in the area of heterocyclic chemistry, are well known. Although simple Pyrimidines have always been formulated as 4 with the IUPAC numbering shown, uracil (8) and its derivatives have been numbered frequently with their oxy substituents at the 2- and 6-positions to conform with the exceptional numbering system of purine (9), still unaccountably recommended by IUPAC;6166 cytosine (10, R = H) and its derivatives have suffered also from a similar ambiguity, but mainly in the older literature. The most serious confusion results from N- substitution in association with such trivial names. For example, methylation of cytosine (10, R = H) gives the product (10, R = Me), then known as 1- or 3- methylcytosine according to whether the amino group is considered to occupy the 4- or 6-position: in 1955, the Journal of the Chemical Society used one system on page 214, but the other on page 855! For this reason, trivial names are avoided in most of this book, for example, by naming the methylated cytosine (10, R = Me) as 4-amino-l-methy1-2(1H)-pyrimidinone. The naming of nitrogenous heterocycles bearing u- and/or y-tautomeric groups is always confusing: for example, what is the tautomeric compound (11) to be called? Fortunately, it is an experimental fact that most such compounds exist predominantly with the mobile hydrogen attached to the u-nitrogen atom, so that they are named accordingly (at least in this book): thus compound 11 is known as 4(3H)-pyrimidinone. In contrast, compounds such as 12 invariably retain their mobile hydrogen on the exocyclic nitrogen, so that the amine (12) is named as 4-pyrimidinamine rather than 4(3H)-pyrimidinimine or the like.
eBook - PDF- Desmond J. Brown(Author)
- 2009(Publication Date)
- Wiley-Interscience(Publisher)
Library of Congress Cataloging in Publication Data: (Revised for volume 16, supplement 11) Brown, D. J. The Pyrimidines. 24 (The Chemistry of heterocyclic compounds, v. 16) Accompanied by “Supplement I- ” ( v. : ill. ; cm.) published: New York : Wiley-Interscience, Includes bibliographies and indexes. 1. Pyrimidines. I. Title. 1970- QD401.B866 547l.593 61-9039 ISBN 0-471-38116-0 (v. 1) To My Research Students Past and Present who taught me far more about Pyrimidine chemistry than I ever taught them: BRIAN ENGLAND PHILFORD ROY FOSTER JOHN HOSKINS KAZU IENAGA NOEL JACOBSEN TZOONG LEE JANICE LYALL BOB LYNN KENYA MORI MIKE PADDON-ROW TOMTEITEI KAZUO SHINOZUKA TAKASHI SUGIMOTO PAUL WARING The Chemistry of Heterocyclic Compounds The chemistry of heterocyclic compounds is one of the most complex branches of organic chemistry. It is equally interesting for its theoretical implications, for the diversity of its synthetic procedures, and for the physiological and industrial significance of heterocyclic compounds. A field of such importance and intrinsic difficulty should be made as readily accessible as possible, and the lack of a modern detailed and comprehensive presentation of heterocyclic chemistry is therefore keenly felt. It is the intention of the present series to fill this gap by expert presentations of the various branches of heterocyclic chemistry. The subdivisions have been designed to cover the field in its entirety by monographs which reflect the importance and the interrelations of the various compounds, and accommodate the specific interests of the authors. In order to continue to make heterocyclic chemistry “as readily accessible as possible”, new editions are planned for those areas where the respective volumes in the first edition have become obsolete by overwhelming progress.
- Erwin Klingsberg(Author)
- 2009(Publication Date)
- Wiley-Interscience(Publisher)
PYRIDINE and Its Derivatives Part One Erwin Klingsberg, Editor Atircricon Cyanamid vompany, Bound Brook, New Jersey 1960 INTERSCIENCE PUBLISHERS, INC., NEW YORK INTERSCIENCE PUBLISHERS LTD., LONDON PYRIDINE AND ITS DERIVATIVES In Four Parts PART ONE Tbii ic Part One of tbc fonrtrcntb volams finblirbcrl in tbr wries THE CHEMISTRY OF HETEROCYCLIC COMPOUNDS ~~ ~ THE CHEMISTRY OF HETEROCYCLIC COMPOUNDS A SERIES OF MONOGRAPHS ARNOLD WEISSBERGER, Consulting Editor 1). ContriOutors to This Pnrt R. A. Barnes Rutgers, The Slate University, New Rrunswick, New Jersey Frederick Brody American Cyanamid Compnny, Bound Brook, New Jersey Philip R. Ruby American Cyanamid Company. Rotcnd Brook, New Jersey PYRIDINE and Its Derivatives Part One Erwin Klingsberg, Editor Atircricon Cyanamid vompany, Bound Brook, New Jersey 1960 INTERSCIENCE PUBLISHERS, INC., NEW YORK INTERSCIENCE PUBLISHERS LTD., LONDON Copyright 0 1960 by Interscience Publishers, Inc. All Rights Reserved Library of Congress Catalog Card Number 59-13038 INTERSCIENCE PUBLISHERS, INC., 250 Fifth Avenue, New York 1, N. Y. For Great Britain and Northern Ireland: Interscience Publishers, Ltd., 88/90 Chancery Lane, London, W.C. 2 The Chemistry of Heterocyclic Compounds The chemistry of heterocyclic compounds is one OE the most com- plex branches of organic chemistry. It is equally interesting for its theoretical implications, for the diversity of its synthetic procedures, and for the physiological and industrial significance of heterocyclic compounds. A field of such importance and intrinsic difficulty should be made as readily accessible as possible, and the lack of a modern detailed and comprehensive presentation of heterocyclic chemistry is there- fore keenly felt. It is the intention of the present series to fill this gap by expert presentations of the various branches of heterocyclic chemistry.
- Erwin Klingsberg(Author)
- 2009(Publication Date)
- Wiley-Interscience(Publisher)
PYRIDINE and Its Derivatives Part Two Erwin Klingsberg, Editor American Cyanamid Company, Bound Brook, New ]my 1961 INTERSCIENCE PUBLISHERS, INC., NEW YORK INTERSCIENCE PUBLISHERS LTD., LONDON PYRIDINE AND ITS DERIVATIVES In Four Parts PART TWO Tbir is P d Two of tbe fowrterntb volume gwbksbed in tbr series THE CHEMISTRY OF HETEROCYCLIC COMPOUNDS THE CHEMISTRY OF HETEROCYCLIC COMPOUNDS A SERIES OF MONOGRAPHS ARNOLD WEISSBERGER, Consulting Edifor 0 . Contributors to This Part Holly E. Menel Merck Sharp and Dohtne Research Laboratories, Rahway, New Jersv Renat H. Minoni Ciba Pharmaceutical Products, Inc., Summit, New Jersey Elliott N . Shaw Rochefelkr Institute for Medical Research, New York, New York Leon E. Teaenbaum Nepera Chemical Company, Yonkers, New York Harty L. Yale Squib6 Institute for Medical Research, New Brunswich, New Jersey PYRIDINE and Its Derivatives Part Two Erwin Klingsberg, Editor American Cyanamid Company, Bound Brook, New ]my 1961 INTERSCIENCE PUBLISHERS, INC., NEW YORK INTERSCIENCE PUBLISHERS LTD., LONDON Copyright 0 1961 by Interscience Publishers, Inc. All Rights Reserved Library of Congrru Catalog Card Number 59-13038 INTERSCIENCE PUBLISHERS, INC., 250 Fifth Avenue, New York 1. N. Y. For Great Britain and Northern Ireland: I n t d m c e Publishers, Ltd.. 88/90 Chancery Lane. London, W.C. 2 The Chemistry of Heterocyclic Compounds The chemistry of heterocyclic compounds is one of the most com- plex branches of organic chemistry. It is equally interesting for its theoretical implications, for the diversity of its synthetic procedures, and for the physiological and industrial significance of heterocyclic compounds. A field of such importance and intrinsic difficulty should be made as readily accessible as possible, and the lack of a modern detailed and comprehensive presentation of heterocyclic chemistry is there- fore keenly felt.
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